Variant report

Variant	rs12224436
Chromosome Location	chr11:8815825-8815826
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8708277..8712745-chr11:8814108..8817920,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10743093	0.81[CEU][hapmap]
rs10769947	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10769948	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10769955	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769957	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769958	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10769967	0.82[CEU][hapmap]
rs10769970	0.82[CEU][hapmap]
rs10769971	0.81[CEU][hapmap]
rs10769973	0.82[CEU][hapmap]
rs10840130	0.82[AMR][1000 genomes]
rs10840134	0.86[CEU][hapmap]
rs10840141	0.82[CEU][hapmap]
rs10840142	0.82[CEU][hapmap]
rs10840148	0.81[CEU][hapmap]
rs11042055	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042059	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042060	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042067	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11042069	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042078	0.81[CEU][hapmap]
rs11042079	0.81[AMR][1000 genomes]
rs11042082	0.80[AMR][1000 genomes]
rs11042103	0.82[CEU][hapmap]
rs11603841	0.80[CEU][hapmap]
rs12421789	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16905815	0.91[YRI][hapmap]
rs2316865	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568043	0.81[CEU][hapmap]
rs2568061	0.81[CEU][hapmap]
rs2568065	0.81[CEU][hapmap]
rs2568090	0.81[CEU][hapmap]
rs2742545	0.81[CEU][hapmap]
rs3763918	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3794153	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4554887	0.80[AMR][1000 genomes]
rs4579928	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4910062	0.80[CEU][hapmap]
rs4929911	0.95[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929912	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929914	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4929916	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61876187	0.81[AMR][1000 genomes]
rs6484484	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484494	0.80[YRI][hapmap]
rs6484496	0.89[EUR][1000 genomes]
rs7107867	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7119939	0.80[CEU][hapmap]
rs7123429	0.82[CEU][hapmap]
rs7129667	0.95[EUR][1000 genomes]
rs7937298	0.82[CEU][hapmap]
rs7944560	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945378	0.90[YRI][hapmap]
rs7945705	0.81[CEU][hapmap]
rs7949286	0.91[YRI][hapmap]
rs905290	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12224436	TMEM9B-AS1	cis	lung	GTEx
rs12224436	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8797800-8827200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:8800800-8822400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:8800800-8825800	Weak transcription	Brain Angular Gyrus	brain
4	chr11:8800800-8827400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:8801600-8820000	Weak transcription	HSMMtube	muscle
6	chr11:8801600-8827400	Weak transcription	Esophagus	oesophagus
7	chr11:8802000-8816000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr11:8802200-8819200	Weak transcription	NH-A	brain
9	chr11:8802800-8816000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:8803000-8820600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:8808600-8819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:8808800-8816000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:8808800-8816200	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:8809000-8816000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:8809000-8816200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:8809000-8830200	Weak transcription	Fetal Brain Male	brain
17	chr11:8809200-8816200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:8809200-8826600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:8809200-8829200	Weak transcription	Fetal Kidney	kidney
20	chr11:8810400-8816200	Weak transcription	NHLF	lung
21	chr11:8810600-8816000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:8810600-8820600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:8811800-8827000	Weak transcription	HMEC	breast
24	chr11:8811800-8828600	Weak transcription	Hela-S3	cervix
25	chr11:8811800-8828800	Weak transcription	Aorta	Aorta
26	chr11:8811800-8830400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr11:8811800-8830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:8812200-8816200	Weak transcription	Fetal Thymus	thymus
29	chr11:8812400-8816000	Weak transcription	Fetal Heart	heart
30	chr11:8812400-8820600	Weak transcription	Right Ventricle	heart
31	chr11:8812800-8816600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:8813800-8817600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr11:8814200-8817000	Enhancers	Rectal Smooth Muscle	rectum
34	chr11:8814200-8817200	Enhancers	Colon Smooth Muscle	Colon
35	chr11:8814200-8828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:8814400-8816400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr11:8814400-8816600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr11:8814600-8817400	Weak transcription	NHEK	skin
39	chr11:8814800-8816000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:8814800-8825400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr11:8815000-8827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:8815200-8816000	Enhancers	Small Intestine	intestine
43	chr11:8815200-8816400	Enhancers	Pancreas	Pancrea
44	chr11:8815200-8817000	Enhancers	Fetal Intestine Large	intestine
45	chr11:8815200-8818200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr11:8815200-8818800	Weak transcription	Adipose Nuclei	Adipose
47	chr11:8815200-8826800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:8815400-8817000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
49	chr11:8815400-8818000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:8815400-8818600	Weak transcription	Monocytes-CD14+_RO01746	blood

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